The structures of isomeric by-products of technical perfluorooctane sulfonate (PFOS, C8F17SO) were characterized by high-performance liquid chromatography coupled to mass spectrometry. Ion trap (IT) as well as triple quadrupole (TQ) tandem mass spectrometry (MS/MS) identified ten PFOS isomers with best results being achieved by ion trap MS/MS. In addition to the linear isomer, the main by-products were isomers with geminal diperfluoromethyl groups and perfluoromethyl-substituted compounds. Purified fractions of the perfluoromethyl isomers allowed the elucidation of structures and the assignment of the retention times of perfluoroisopropyl-, 5-perfluoromethyl-, 4-perfluoromethyl-, 3-perfluoromethyl- and 1-perfluoromethyl-PFOS. The concentration of 2-perfluoromethyl-PFOS was too low in technical PFOS for a proper identification. Retention times of the geminal substituted diperfluoromethyl isomers could not be properly assigned due to co-elutions. The number and position of the CF3 groups can be derived from the MS/MS spectra, which allow an unequivocal identification of the isomers. TQ-MS/MS also allowed us to identify most of the isomers. Copyright © 2006 John Wiley & Sons, Ltd.